A New Rapid DNA Test Helped Save a Kid From an Obscure Infection

When we think of medicine, we usually think of the treatment: drugs, surgery, therapy. But before all that comes the diagnosis -- a tricky proposition when symptoms are confusing and information scant. Now for the first time ever, doctors were able to use rapid DNA sequencing to identify an obscure bacterium in time to save a boy's life.

"This is an absolutely great story -- it's a tremendous tour de force," a researcher not involved in the study told the New York Times. For weeks, the brain of a 14-year-old boy had been swelling, and he fell into a coma. What he had was encephalitis, which has enough syllables to sound like a diagnosis but really just means an infection in the brain, pathogen unknown. Encephalitis could be caused by anything from a bacterium to a virus to a fungus.

So his doctors turned to DNA sequencing. Using a method called unbiased next-generation sequencing, they extracted all DNA from the boy's cerebrospinal fluid and searched for fragments belonging to a pathogen. Within 48 hours, they found the culprit, an obscure bacterium called Leptospira santarosai. Diagnosis in hand, the doctors knew how to treat the infection.

While DNA sequencing has certainly identified pathogens in patients before, it had been far too slow for emergency situations like this. Sifting through millions of fragments takes a lot of computer power and, crucially, time. The new advance is a piece of software that analyses the DNA more quickly than ever before. There are still challenges, of course, such as there being so many microbes living inside us; it may not be always be easy to identify the exact pathogen.

But since the the human genome sequence was triumphantly announced now over 13 years ago, DNA sequencing has become much cheaper and quicker. Large-scale sequencing is finally making it out of the lab and into the hospital. A couple of years ago, a Wisconsin boy's rare genetic disease was diagnosed by sequencing his whole genome. We will be seeing more stories like this to come. [NEJM via New York Times]